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Sunday, January 27, 2008

Diatoms -some of which are so tiny that 30 can fit across the width of a human hair

Could Tiny Diatoms Help Offset Global Warming?

Diatoms -- some of which are so tiny that 30 can fit across the width of a human hair -- are so numerous that they are among the key organisms taking the greenhouse gas carbon dioxide out of the Earth's atmosphere.The shells of diatoms are so heavy that when they die in the oceans they typically sink to watery graves on the seafloor, taking carbon out of the surface waters and locking it into sediments below.

Scientists have reported the discovery of whole subsets of genes and proteins that govern how one species of diatom builds its shell. For oceanographers, the work might one day help them understand how thousands of different kinds of diatoms -- and their ability to remove carbon dioxide from the atmosphere -- might be affected by something like global climate change. Material scientists involved in the work are interested in the possibilities of manipulating the genes responsible for silica production as a way of fabricating more efficient computer chips.

Diatoms, most of which are far too tiny to see without magnification, are incredibly important in the global carbon cycle, says Thomas Mock, a University of Washington postdoctoral researcher in oceanography and lead author of the paper. During photosynthesis, diatoms turn carbon dioxide into organic carbon and, in the process, generate oxygen. They are responsible for 40 percent of the organic carbon produced in the world's oceans each year.

The new work took advantage of the genomic map of the diatom Thalassiosira pseudonana published in 2004 by a team led by UW oceanography professor Virginia Armbrust, who is corresponding author of the new PNAS paper.* Thalassiosira pseudonana is encased in a hatbox-shaped shell comprised of a rigid cell wall, made mainly of silica and delicately marked with pores in patterns distinctive enough for scientists to tell it from other diatoms.

Armed with the genomic map, the researchers changed environmental conditions in laboratory cultures of Thalassiosira pseudonana, for example limiting the amount of silicon and changing the temperatures. Then researchers used what's called "whole genome expression profiling" to determine which parts of the genome were triggered to compensate.

Think of a plant on a windowsill that starts getting a lot more sunlight, Mock says. The new set of conditions will cause genes in the plant to turn on and off to help the plant acclimate to the increased light as best it can.

Scientists since the late 1990s have found only a handful of genes that influence diatom shell formation. The work with Thalassiosira pseudonana identified large, previously unknown subsets. A set of 75 genes, for example, was triggered to compensate when silicon was limited.

The researchers were surprised to find another subset of 84 genes triggered when either silicon or iron were limited, suggesting that these two pathways were somehow linked. Under low-iron conditions, the diatoms grew more slowly and genes involved in the production of the silica shell were triggered. Individual diatoms also tended to clump together under those conditions, making them even heavier and more likely to sink.

The response of thin and thick cell walls depending on the amount of iron available had been observed at sea but "no one had a clue about the molecular basis," Mock says.

Considering that 30 percent of the world's oceans are iron-poor, some scientists have suggested fertilizing such areas with iron so diatoms become more numerous and absorb more carbon dioxide from the atmosphere, thus putting the brakes on global warming. If, however, adding iron causes diatoms to change the thickness of their shells then perhaps they won't be as likely to sink and instead would remain in the upper ocean where the carbon they contain might be released back to the atmosphere as they decay or are eaten.

"Iron increases primary production by diatoms but our study adds another concern about the efficiency of iron fertilization," Mock says.

Along with helping scientists understand implications for climate change and absorption of carbon dioxide, diatoms can manipulate silica in ways that engineers can only dream about.

University of Wisconsin professor Michael Sussman, the co-corresponding author on the paper, says the new findings will help his group start manipulating the genes responsible for silica production and potentially harness them to produce lines on computer chips. This could vastly increase chip speed because diatoms are capable of producing lines much smaller than current technology allows, he says.

*This research was published recently in the online edition of the Proceedings of the National Academy of Sciences.

Other co-authors from the University of Washington are Vaughn Iverson, Chris Berthiaume, Karie Holtermann and Colleen Durkin; from Systemix Institute is Manoj Pratim Samanta; and from University of Wisconsin are Matthew Robinson, Sandra Splinter BonDurant, Kathryn Richmond, Matthew Rodesch, Toivo Kallas, Edward Huttlin and Franceso Cerrina.

Funding for the research came from the Gordon and Betty Moore Foundation, National Science Foundation, German Academic Exchange Service, National Institutes of Health Genomic Sciences Training Center and the University of Wisconsin.

more....

Tiny Phytoplankton Could Be Harboring the Next Big breakthrough In Computer Chips.Denizens of oceans, lakes and even wet soil, diatoms are unicellular algae that encase themselves in intricately patterned, glass-like shells. Curiously, these tiny phytoplankton could be harboring the next big breakthrough in computer chips.

Diatoms build their hard cell walls by laying down submicron-sized lines of silica, a compound related to the key material of the semiconductor industry--silicon. "If we can genetically control that process, we would have a whole new way of performing the nanofabrication used to make computer chips," says Michael Sussman, a University of Wisconsin-Madison biochemistry professor and director of the UW-Madison's Biotechnology Center.To that end, a team led by Sussman and diatom expert Virginia Armbrust of the University of Washington has reported finding a set of 75 genes specifically involved in silica bioprocessing in the diatom Thalassiosira pseudonana, as published January 21 in the online Early Edition of the Proceedings of the National Academy of Sciences. Armbrust, an oceanography professor who studies the ecological role of diatoms, headed up the effort to sequence the genome of T. pseudonana, which was completed in 2004.

The new data will enable Sussman to start manipulating the genes responsible for silica production and potentially harness them to produce lines on computer chips. This could vastly increase chip speed, Sussman says, because diatoms are capable of producing lines much smaller than current technology allows.

"The semiconductor industry has been able to double the density of transistors on computer chips every few years. They've been doing that using photolithographic techniques for the past 30 years," explains Sussman. "But they are actually hitting a wall now because they're getting down to the resolution of visible light."

Before diatoms were appreciated for their engineering prowess, they interested ecologists for their role in the planet's carbon cycle. These photosynthetic cells soak up carbon dioxide and then fall to the ocean floor. They account for upwards of 20 percent of the carbon dioxide that is removed from the atmosphere each year, an amount comparable to that removed by all of the planet's rainforests combined.

"We want to see which genes express under different environmental conditions because these organisms are so important in global carbon cycling," explains Thomas Mock, a postdoctoral researcher in Armbrust's lab and the paper's first author.

But research on these algae has uncovered other enticing possibilities. As he learned about diatoms, Sussman became intrigued by the fact that each species of diatom--there may be around 100,000 of them--is believed to sport a uniquely designed cell wall.

To determine which genes are involved in creating those distinctive patterns, the research team used a DNA chip developed by Sussman, UW-Madison electrical engineer Franco Cerrina and UW-Madison geneticist Fred Blattner, the three founders of the biotechnology company NimbleGen. Put simply, the chip allows scientists to see which genes are involved in a given cellular process. In this case, the chip identified genes that responded when diatoms were grown in low levels of silicic acid, the raw material they use to make silica.

Of the 30 genes that increased their expression the most during silicic acid starvation, 25 are completely new, displaying no similarities to known genes.

"Now we know which of the organism's 13,000 genes are most likely to be involved in silica bioprocessing. Now we can zero in on those top 30 genes and start genetically manipulating them and see what happens," says Sussman.

For his part, Sussman is optimistic that in the long run these findings will help him improve the DNA chip he helped develop -- the very one used to gather data for this research project. "It's like the Lion King song," he says. "You know, 'the circle of life.'"